The efforts of the Human Genome Project opened a broader window to the human genome. The work to further unlock the human genome is ongoing. The HapMap (Haplotype Map) Project is a global scientific effort directed at discovering genetic variants that lead to disease by comparing genomic information from people without a particular disease to those with that disease. Alleles, one or more forms of a DNA sequence for a particular gene, can contain one or more different genetic variants. Identifying haplotypes, or combinations of alleles at different locations, or loci, on a particular chromosome is a main focus of the HapMap Project. Identified haplotypes where the two groups differ might correlate to locations of genetic anomalies that cause disease. As such, HapMap results will help to describe the common patterns of genetic variation in humans and whether those variations are potentially correlated to disease. Research efforts in determining haplotypes will help illuminate the common patterns of genetic variation in humans and whether those variations are potentially correlated to a particular disease. Indeed, many researchers agree that haplotyping a genome will be advantageous, if not essential, in relating genetic variation to phenotype and disease. Further, a particular haplotype may be correlated to the success or failure of a treatment regimen and as such could be useful in helping a clinician decide on a therapeutic regimen for a particular individual that might have the highest degree of success in disease eradication in that individual.
However, there are many technical challenges associated with genomic haplotyping. For example, next generation sequencing technologies while increasing the capacity and accuracy of sequencing efforts, in many cases result in short sequence reads, for example several commercial platforms currently output per fragment reads that are less than 400 nucleotides long. If two or more genetic variants located on a chromosome are further apart than the sequence read length, even if that read length is thousands of base pairs long, it may be difficult if not impossible to define a haplotype. As such, what are needed are methods and compositions that allow for haplotyping, in particular for genetic variants that are farther apart on a chromosome than the sequenced length of a piece of DNA upon which they are found.